Variant report

Variant	rs11721403
Chromosome Location	chr4:110693569-110693570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10016598	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10049804	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10857001	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11734208	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11943677	0.81[ASN][1000 genomes]
rs13129180	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs1990250	0.83[ASW][hapmap]
rs3188897	0.92[ASW][hapmap]
rs4469075	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4541508	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4698784	0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6533457	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841303	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7438763	0.83[ASW][hapmap]
rs7438961	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7439356	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7440009	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7675460	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9654197	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11721403	LRIT3	cis	cerebellum	SCAN
rs11721403	CYP2U1	cis	parietal	SCAN
rs11721403	RRH	cis	parietal	SCAN
rs11721403	RRH	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110687800-110694400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:110691400-110694200	Weak transcription	HepG2	liver
3	chr4:110691400-110695400	Weak transcription	Liver	Liver
4	chr4:110691600-110694600	Weak transcription	Fetal Intestine Small	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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